Package index • ampseqQC

QC report

read_mad4hatter_results(): Read Mad4hatter results
read_manifest(): Read a sample manifest
standardise_illumina_sample_name(): Remove Illumina FASTQ suffixes from sample names
sample_name_mismatches() check_sample_names(): Compare manifest and pipeline sample names

Map pools to reactions and choose targets to exclude from QC.

panel_settings(): Panel settings
default_panel_settings(): Default panel settings for MAD4HatTeR and PfPHAST
assign_reactions(): Assign targets to reactions
summarise_pools(): Summarise pools in a run
qc_excluded_targets(): Targets excluded from QC

merge_sample_coverage(): Add the manifest to sample coverage
merge_amplicon_coverage(): Add the manifest and reactions to amplicon coverage
count_targets_per_reaction(): Count targets per reaction
summarise_samples(): Summarise amplification success per sample and reaction
generate_reprep_repool_table(): Classify samples as pass, repool or reprep
fill_missing_data(): Add samples and reactions with no data
samples_with_status(): Samples with a given QC status
sample_qc_status(): Sample-level QC status
qc_status_counts(): Overall QC counts
qc_summary_by_batch() qc_summary_table(): QC status by batch

add_allele_frequency(): Add within-sample allele frequency
summarise_positive_controls(): Summarise alleles per target in positive controls
negative_control_amplicons(): Negative control amplicon coverage
negative_control_targets_over_threshold(): Negative control targets above a read threshold
summarise_negative_control_targets(): Total reads per target across negative controls

filter_allele_table(): Filter an allele table
allele_table_group_cols(): Locus columns for Mad4hatter output tables
sample_counts_by_file(): Number of samples in each input file
samples_missing_from_allele_data(): Why manifest samples are missing from the allele data
missing_samples_report(): Samples in the manifest missing from the allele data
missing_targets_report(): Targets in the panel missing from the allele data

create_plate_template(): Plate template
plot_plate() plot_plate_layouts(): Plate layout plots
generate_dimer_plot(): Primer dimer content
generate_balancing_plot(): Balancing across batches
generate_reads_by_amplification_success_plot() generate_reads_by_amplification_success_plots(): Sample reads against amplification success
generate_parasitemia_by_amplification_success_plot() generate_parasitemia_by_amplification_success_plots(): Parasitemia against amplification success
plot_plate_with_feature() plot_plate_heat_maps(): Plate heatmaps
plot_positive_control_alleles(): Alleles per target in positive controls
plot_negative_control_histogram(): Read distribution per negative control
negative_control_plot_height(): Figure height for negative control histograms
plot_negative_control_target_reads(): Total reads per target across negative controls
plot_qc_status_by_batch(): QC status by batch

Helpers used by the report template.